MolNFT v1 · #72444 · protein
Crystal structure of an imelysin peptidase (BACOVA_03801) from bacteroides ovatus at 1.44 a resolution
3N8U: “Crystal structure of an imelysin peptidase (BACOVA_03801) from bacteroides ovatus at 1.44 a resolution”. X-ray diffraction, 2 ligands (MG, CL), 2 pockets (best druggability 0.54). MolNFT v1 #72444 on GenesisL1: 3D structure, binding…
- PDB
- 3N8U
- Type
- protein
- Length
- 706 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Imelysin peptidase
- UniProt
- A7M120
- Ligands
- MG, CL
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Imelysin peptidase | protein | 352 | 72% helix, 1% strand | A7M120 |
| B | Imelysin peptidase | protein | 354 | 72% helix, 2% strand | A7M120 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.54 | 0.75 | 45 | MG |
| 2 | 126 | 0.41 | 0.75 | 20 | MG |
Interfaces
1 interface between chains.
- A–B · 278 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3N8U · Crystal structure of an imelysin peptidase (BACOVA_03801) from Bacteroides ovatus at 1.44… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A7M120
- Elsewhere: RCSB PDB 3N8U · PDBe 3N8U · UniProt A7M120
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